- recipe nomadic
Mobile sequencing and analysis in real-time
- Homepage:
- Developer docs:
- License:
MIT
- Recipe:
Nomadic is a real-time bioinformatics pipeline and dashboard for nanopore sequencing data. While sequencing is still ongoing, it performs read mapping and sample quality control, as well as variant calling and annotation. This information is displayed in real-time to a graphical dashboard that has interactive features.
- package nomadic¶
- versions:
0.5.0-0,0.4.0-0- depends bcftools:
>=1.20- depends bedtools:
- depends click:
- depends dash:
- depends i18nice:
- depends minimap2:
- depends numpy:
- depends pandas:
- depends platformdirs:
- depends pysam:
- depends python:
>=3.10- depends pyyaml:
- depends samtools:
>=1.20- depends seaborn:
- requirements:
- additional platforms:
Installation
You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).
While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.
Given that you already have a conda environment in which you want to have this package, install with:
mamba install nomadic and update with:: mamba update nomadic
To create a new environment, run:
mamba create --name myenvname nomadic
with
myenvnamebeing a reasonable name for the environment (see e.g. the mamba docs for details and further options).Alternatively, use the docker container:
docker pull quay.io/biocontainers/nomadic:<tag> (see `nomadic/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/nomadic/README.html)
